Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_012417	674	786	113	2 [1]	[1] 2	USA300HOU_RS14890	replication protein

TTGTAAGTGATTTAGAAAAAGGTTTGTATCGAAAACGTATGTTAAGTTATGGTGGATTGCTTAAACAAAAACATAAAATTTTAAACTTAGACGATGTCGAAGATGGTAATTTGATTAATGCAAGTGATGAAGATAAAACAACAGACGAAGAAGAAAA  >  NC_012417/779‑935         |                                                                                                                                                     ttGTAAGTGATTTAGAAAAAGGTTTGTATCGAAAACGTATGTTAAGTTATGGTGGATTGCTTAAACAAAAACATAAAATTTTAAACTTAGACGATGTCGAAGATGGTAATTTGATTAATGCAAGTGATGAAGATAAAACAACAGACgaa          <  2:230166/149‑1 (MQ=40)         gATTTAGAAAAAGGTTTGTATCGAAAACGTATGTTAAGTTATGGTGGATTGCTTAAACAAAAACATAAAATTTTAAACTTAGACGATGTCGAAGATGGTAATTTGATTAATGCAAGGGATGAAGATAAAACAACAGACGAAGAAGaaaa  <  1:1622161/149‑1 (MQ=255)         |                                                                                                                                                     TTGTAAGTGATTTAGAAAAAGGTTTGTATCGAAAACGTATGTTAAGTTATGGTGGATTGCTTAAACAAAAACATAAAATTTTAAACTTAGACGATGTCGAAGATGGTAATTTGATTAATGCAAGTGATGAAGATAAAACAACAGACGAAGAAGAAAA  >  NC_012417/779‑935

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑